src/jalview/gui/FeatureRenderer.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.gui;\r
  20 \r
  21 import jalview.datamodel.*;\r
  22 \r
  23 import java.awt.*;\r
  24 \r
  25 import java.util.*;\r
  26 \r
  27 import java.awt.image.*;\r
  28 \r
  29 \r
  30 /**\r
  31  * DOCUMENT ME!\r
  32  *\r
  33  * @author $author$\r
  34  * @version $Revision$\r
  35  */\r
  36 public class FeatureRenderer\r
  37 {\r
  38     AlignViewport av;\r
  39     Color resBoxColour;\r
  40     float transparency = 1.0f;\r
  41     FontMetrics fm;\r
  42     int charOffset;\r
  43 \r
  44     Hashtable featureColours = new Hashtable();\r
  45 \r
  46 \r
  47     // A higher level for grouping features of a\r
  48    // particular type\r
  49     Hashtable featureGroups = null;\r
  50 \r
  51     // This is actually an Integer held in the hashtable,\r
  52     // Retrieved using the key feature type\r
  53     Object currentColour;\r
  54 \r
  55     String [] renderOrder;\r
  56 \r
  57     boolean newFeatureAdded = false;\r
  58 \r
  59 \r
  60     /**\r
  61      * Creates a new FeatureRenderer object.\r
  62      *\r
  63      * @param av DOCUMENT ME!\r
  64      */\r
  65     public FeatureRenderer(AlignViewport av)\r
  66     {\r
  67         this.av = av;\r
  68     }\r
  69 \r
  70     public void transferSettings(FeatureRenderer fr)\r
  71     {\r
  72       renderOrder = fr.renderOrder;\r
  73       featureGroups = fr.featureGroups;\r
  74       featureColours = fr.featureColours;\r
  75       transparency =  fr.transparency;\r
  76     }\r
  77 \r
  78     BufferedImage offscreenImage;\r
  79     boolean offscreenRender = false;\r
  80     public Color findFeatureColour(Color initialCol, SequenceI seq, int res)\r
  81     {\r
  82       return new Color( findFeatureColour (initialCol.getRGB(),\r
  83                         seq, res ));\r
  84     }\r
  85 \r
  86     /**\r
  87      * This is used by the Molecule Viewer and Overview to\r
  88      * get the accurate colourof the rendered sequence\r
  89      */\r
  90     public int findFeatureColour(int initialCol, SequenceI seq, int column)\r
  91     {\r
  92       if(!av.showSequenceFeatures)\r
  93         return initialCol;\r
  94 \r
  95       if(seq!=lastSeq)\r
  96       {\r
  97         lastSeq = seq;\r
  98         sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();\r
  99         if(sequenceFeatures==null)\r
 100           return initialCol;\r
 101 \r
 102         sfSize = sequenceFeatures.length;\r
 103       }\r
 104 \r
 105       if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))\r
 106         return Color.white.getRGB();\r
 107 \r
 108 \r
 109       //Only bother making an offscreen image if transparency is applied\r
 110       if(transparency!=1.0f && offscreenImage==null)\r
 111       {\r
 112         offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB);\r
 113       }\r
 114 \r
 115       currentColour = null;\r
 116 \r
 117       offscreenRender = true;\r
 118 \r
 119       if(offscreenImage!=null)\r
 120       {\r
 121         offscreenImage.setRGB(0,0,initialCol);\r
 122         drawSequence(offscreenImage.getGraphics(),\r
 123                      lastSeq,\r
 124                      column,column,0);\r
 125 \r
 126         return offscreenImage.getRGB(0,0);\r
 127       }\r
 128       else\r
 129       {\r
 130         drawSequence(null,\r
 131                     lastSeq,\r
 132                     lastSeq.findPosition(column),\r
 133                     -1, -1);\r
 134 \r
 135         if (currentColour == null)\r
 136           return initialCol;\r
 137         else\r
 138           return  ((Integer)currentColour).intValue();\r
 139       }\r
 140 \r
 141 \r
 142     }\r
 143 \r
 144 \r
 145     /**\r
 146      * DOCUMENT ME!\r
 147      *\r
 148      * @param g DOCUMENT ME!\r
 149      * @param seq DOCUMENT ME!\r
 150      * @param sg DOCUMENT ME!\r
 151      * @param start DOCUMENT ME!\r
 152      * @param end DOCUMENT ME!\r
 153      * @param x1 DOCUMENT ME!\r
 154      * @param y1 DOCUMENT ME!\r
 155      * @param width DOCUMENT ME!\r
 156      * @param height DOCUMENT ME!\r
 157      */\r
 158    // String type;\r
 159    // SequenceFeature sf;\r
 160     SequenceI lastSeq;\r
 161     SequenceFeature [] sequenceFeatures;\r
 162     int sfSize, sfindex, spos, epos;\r
 163 \r
 164     public void drawSequence(Graphics g, SequenceI seq,\r
 165                              int start, int end, int y1)\r
 166     {\r
 167       if ( seq.getDatasetSequence().getSequenceFeatures() == null\r
 168           || seq.getDatasetSequence().getSequenceFeatures().length==0)\r
 169         return;\r
 170 \r
 171 \r
 172       if(g!=null)\r
 173         fm = g.getFontMetrics();\r
 174 \r
 175 \r
 176       if (av.featuresDisplayed == null\r
 177           || renderOrder==null\r
 178           || newFeatureAdded)\r
 179        {\r
 180          findAllFeatures();\r
 181          if(av.featuresDisplayed.size()<1)\r
 182            return;\r
 183 \r
 184          sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
 185          sfSize = sequenceFeatures.length;\r
 186        }\r
 187 \r
 188        if(lastSeq==null || seq!=lastSeq)\r
 189       {\r
 190         lastSeq = seq;\r
 191         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
 192         sfSize = sequenceFeatures.length;\r
 193       }\r
 194 \r
 195 \r
 196       if (transparency != 1 && g!=null)\r
 197       {\r
 198         Graphics2D g2 = (Graphics2D) g;\r
 199         g2.setComposite(\r
 200             AlphaComposite.getInstance(\r
 201                 AlphaComposite.SRC_OVER, transparency));\r
 202       }\r
 203 \r
 204       if(!offscreenRender)\r
 205       {\r
 206         spos = lastSeq.findPosition(start);\r
 207         epos = lastSeq.findPosition(end);\r
 208       }\r
 209 \r
 210 \r
 211       String type;\r
 212       for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)\r
 213        {\r
 214         type =  renderOrder[renderIndex];\r
 215 \r
 216         if(!av.featuresDisplayed.containsKey(type))\r
 217           continue;\r
 218 \r
 219         // loop through all features in sequence to find\r
 220         // current feature to render\r
 221         for (sfindex = 0; sfindex < sfSize; sfindex++)\r
 222         {\r
 223           if(sequenceFeatures.length<=sfindex)\r
 224           {\r
 225             continue;\r
 226           }\r
 227           if (!sequenceFeatures[sfindex].type.equals(type))\r
 228             continue;\r
 229 \r
 230           if (featureGroups != null\r
 231               && sequenceFeatures[sfindex].featureGroup != null\r
 232               &&\r
 233               featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
 234               &&\r
 235               ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).\r
 236               booleanValue())\r
 237           {\r
 238             continue;\r
 239           }\r
 240 \r
 241           if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos\r
 242                             || sequenceFeatures[sfindex].getEnd() < spos))\r
 243             continue;\r
 244 \r
 245           if (offscreenRender && offscreenImage==null)\r
 246           {\r
 247             if (sequenceFeatures[sfindex].begin <= start &&\r
 248                 sequenceFeatures[sfindex].end  >= start)\r
 249             {\r
 250               currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
 251                  type);\r
 252             }\r
 253           }\r
 254           else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
 255           {\r
 256 \r
 257             renderFeature(g, seq,\r
 258                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 259                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 260                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 261                 sequenceFeatures[sfindex].type)).intValue()),\r
 262                           start, end, y1);\r
 263             renderFeature(g, seq,\r
 264                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 265                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 266                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 267                 sequenceFeatures[sfindex].type)).intValue()),\r
 268                           start, end, y1);\r
 269 \r
 270           }\r
 271           else\r
 272             renderFeature(g, seq,\r
 273                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 274                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 275                           getColour(sequenceFeatures[sfindex].type),\r
 276                           start, end, y1);\r
 277 \r
 278 \r
 279         }\r
 280 \r
 281       }\r
 282 \r
 283         if(transparency!=1.0f && g!=null)\r
 284         {\r
 285           Graphics2D g2 = (Graphics2D) g;\r
 286           g2.setComposite(\r
 287               AlphaComposite.getInstance(\r
 288                   AlphaComposite.SRC_OVER, 1.0f));\r
 289         }\r
 290     }\r
 291 \r
 292 \r
 293     char s;\r
 294     int i;\r
 295     void renderFeature(Graphics g, SequenceI seq,\r
 296                        int fstart, int fend, Color featureColour, int start, int end,  int y1)\r
 297     {\r
 298 \r
 299       if (((fstart <= end) && (fend >= start)))\r
 300       {\r
 301         if (fstart < start)\r
 302         { // fix for if the feature we have starts before the sequence start,\r
 303           fstart = start; // but the feature end is still valid!!\r
 304         }\r
 305 \r
 306         if (fend >= end)\r
 307         {\r
 308           fend = end;\r
 309         }\r
 310           int pady = (y1 + av.charHeight) - av.charHeight / 5;\r
 311           for (i = fstart; i <= fend; i++)\r
 312           {\r
 313             s = seq.getSequence().charAt(i);\r
 314 \r
 315             if (jalview.util.Comparison.isGap(s))\r
 316             {\r
 317               continue;\r
 318             }\r
 319 \r
 320             g.setColor(featureColour);\r
 321 \r
 322             g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);\r
 323 \r
 324             if(offscreenRender || !av.validCharWidth)\r
 325               continue;\r
 326 \r
 327             g.setColor(Color.white);\r
 328             charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
 329             g.drawString(String.valueOf(s),\r
 330                          charOffset + (av.charWidth * (i - start)),\r
 331                          pady);\r
 332 \r
 333           }\r
 334       }\r
 335     }\r
 336 \r
 337     int count = 0;\r
 338     synchronized public void featuresAdded()\r
 339     {\r
 340       newFeatureAdded = true;\r
 341       findAllFeatures();\r
 342       newFeatureAdded = false;\r
 343     }\r
 344 \r
 345    synchronized void findAllFeatures()\r
 346    {\r
 347       jalview.schemes.UserColourScheme ucs = new\r
 348           jalview.schemes.UserColourScheme();\r
 349 \r
 350       if(av.featuresDisplayed==null)\r
 351         av.featuresDisplayed = new Hashtable();\r
 352 \r
 353       av.featuresDisplayed.clear();\r
 354 \r
 355       Vector allfeatures = new Vector();\r
 356       for (int i = 0; i < av.alignment.getHeight(); i++)\r
 357       {\r
 358         SequenceFeature [] features\r
 359             = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
 360 \r
 361         if (features == null)\r
 362           continue;\r
 363 \r
 364         int index = 0;\r
 365         while (index < features.length)\r
 366         {\r
 367           if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
 368           {\r
 369             if(!(features[index].begin == 0 && features[index].end ==0))\r
 370             {\r
 371               // If beginning and end are 0, the feature is for the whole sequence\r
 372               // and we don't want to render the feature in the normal way\r
 373 \r
 374               if (getColour(features[index].getType()) == null)\r
 375               {\r
 376                  featureColours.put(features[index].getType(),\r
 377                                    ucs.createColourFromName(features[index].\r
 378                     getType()));\r
 379               }\r
 380 \r
 381               av.featuresDisplayed.put(features[index].getType(),\r
 382                                        new Integer(getColour(features[index].\r
 383                   getType()).getRGB()));\r
 384               allfeatures.addElement(features[index].getType());\r
 385             }\r
 386           }\r
 387           index++;\r
 388         }\r
 389       }\r
 390 \r
 391       renderOrder = new String[allfeatures.size()];\r
 392       Enumeration en = allfeatures.elements();\r
 393       int i = allfeatures.size()-1;\r
 394       while(en.hasMoreElements())\r
 395       {\r
 396         renderOrder[i] = en.nextElement().toString();\r
 397         i--;\r
 398       }\r
 399     }\r
 400 \r
 401     public Color getColour(String featureType)\r
 402     {\r
 403       Color colour = (Color)featureColours.get(featureType);\r
 404       return colour;\r
 405     }\r
 406 \r
 407 \r
 408     public void addNewFeature(String name, Color col, String group)\r
 409     {\r
 410 \r
 411       setColour(name, col);\r
 412       if(av.featuresDisplayed==null)\r
 413         av.featuresDisplayed = new Hashtable();\r
 414 \r
 415       if(group == null)\r
 416         group = "NOGROUP";\r
 417 \r
 418       av.featuresDisplayed.put(name, new Integer(col.getRGB()));\r
 419     }\r
 420 \r
 421     public void setColour(String featureType, Color col)\r
 422     {\r
 423       featureColours.put(featureType, col);\r
 424     }\r
 425 \r
 426     public void setTransparency(float value)\r
 427     {\r
 428       transparency = value;\r
 429     }\r
 430 \r
 431     public float getTransparency()\r
 432     {\r
 433       return transparency;\r
 434     }\r
 435 \r
 436     public void setFeaturePriority(Object [][] data)\r
 437     {\r
 438       // The feature table will display high priority\r
 439       // features at the top, but theses are the ones\r
 440       // we need to render last, so invert the data\r
 441       if(av.featuresDisplayed!=null)\r
 442         av.featuresDisplayed.clear();\r
 443       else\r
 444         av.featuresDisplayed = new Hashtable();\r
 445 \r
 446       renderOrder = new String[data.length];\r
 447 \r
 448       if (data.length > 0)\r
 449         for (int i = 0; i < data.length; i++)\r
 450         {\r
 451           String type = data[i][0].toString();\r
 452           setColour(type, (Color) data[i][1]);\r
 453           if ( ( (Boolean) data[i][2]).booleanValue())\r
 454           {\r
 455             av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));\r
 456           }\r
 457 \r
 458           renderOrder[data.length - i - 1] = type;\r
 459         }\r
 460 \r
 461     }\r
 462 \r
 463 \r
 464 \r
 465 \r
 466 }\r